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- PDB-6iju: The DNA binding domain of a response regulator ArlR from Staphylo... -

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Basic information

Entry
Database: PDB / ID: 6iju
TitleThe DNA binding domain of a response regulator ArlR from Staphylococcus aureus
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / Response Regulator
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription activator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Response regulator ArlR / DNA-binding response regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHui, Y. / Qing, W.
CitationJournal: To Be Published
Title: The DNA-binding properties and the structure of the DNA-binding domain of the response regulator ArlR from Staphylococcus aureus
Authors: Hui, Y. / Qing, W.
History
DepositionOct 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)11,4041
Polymers11,4041
Non-polymers00
Water57632
1
A: DNA-binding response regulator

A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)22,8082
Polymers22,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2380 Å2
ΔGint-17 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.233, 67.233, 153.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

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Components

#1: Protein DNA-binding response regulator / Response regulator ArlR


Mass: 11403.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W8UAS4, UniProt: Q9KJN4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate trihydrate pH4.5 , 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 7638 / % possible obs: 99.9 % / Redundancy: 36.6 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.875 / Rmerge(I) obs: 0.09 / Net I/σ(I): 50.1
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.566 / Num. unique obs: 406 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YS6

1ys6


Resolution: 2.4→32 Å / SU ML: 0.3449 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.6815 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2407 362 4.74 %
Rwork0.2115 7276 -
obs0.2129 7638 88.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 0 32 834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075814
X-RAY DIFFRACTIONf_angle_d0.87771102
X-RAY DIFFRACTIONf_chiral_restr0.06127
X-RAY DIFFRACTIONf_plane_restr0.0049140
X-RAY DIFFRACTIONf_dihedral_angle_d8.6016491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.2957830.2661705X-RAY DIFFRACTION64.74
2.75-3.460.28421380.23982688X-RAY DIFFRACTION99.79
3.46-320.20891410.18862883X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: -28.3270292522 Å / Origin y: -11.3167791892 Å / Origin z: -10.5573837001 Å
111213212223313233
T0.287991476408 Å20.0854767337678 Å20.0453282419512 Å2-0.301019472031 Å2-0.0107589827422 Å2--0.28592619063 Å2
L1.16782749053 °20.0910897598209 °2-0.7563458372 °2-2.45919012542 °20.0720071142215 °2--4.05690627507 °2
S0.0817683573874 Å °0.170873759504 Å °-0.0825588054568 Å °-0.320395317684 Å °-0.14071342609 Å °-0.302253709077 Å °0.707796344489 Å °0.62180029157 Å °-0.00703482737134 Å °
Refinement TLS groupSelection details: all

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